# Set the working directory to the project folder.
project_folder <- "."
setwd(project_folder)
library(Seurat)
library(ggplot2)
library(ggalluvial)
library(grid)
library(forcats)
library(see)
library(dplyr)
library(gghalves)
library(viridis)
library(stringr)
library(kableExtra)
integrated.obj <- readRDS("integrated.obj.rds")
gammadelta_genes <- c("GZMA", "GZMB", "GZMH", "GZMK", "GZMM", "PRF1", "GNLY", "NKG7",
"CD4", "CD8A", "CD8B", "TRDV1", "TRGV8", "TRG", "TRD")
FeaturePlot(integrated.obj, features = gammadelta_genes, cols = c("#d3d3d3", "#bf1b2cff"))
## Warning in FetchData.Seurat(object = object, vars = c(dims, "ident", features),
## : The following requested variables were not found: TRG, TRD
metadata <- integrated.obj[[]]
metadata$Clusters <- Idents(integrated.obj)
metadata <- metadata[metadata$Class1 == "CAR+", ]
g1 <- ggplot(metadata[metadata$Clusters == "9 Tcells", ], aes(x = Timepoint, fill = Timepoint)) +
geom_bar() + theme_classic()
g1
g2 <- ggplot(metadata[metadata$Clusters == "9 Tcells", ], aes(x = Patient_id, fill = Timepoint)) +
geom_bar(position = position_dodge(preserve = "single")) + theme_classic()
g2
#CustomHeatmap
gens_gammadelta <- c("ZFP36", "CCL4", "PRF1", "GNLY", "NKG7", "KLRF1", "FCGR3A",
"TRGV8", "TRDV1", "TYROBP", "GZMA", "GZMB", "GZMH", "GZMK", "GZMM", "TRDV1",
"TRGV8")
DoHeatmap(integrated.obj, features = gens_gammadelta) + NoLegend()
sessionInfo()
## R version 4.3.0 (2023-04-21)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## time zone: Europe/Madrid
## tzcode source: internal
##
## attached base packages:
## [1] grid stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] kableExtra_1.3.4 stringr_1.5.0 viridis_0.6.3 viridisLite_0.4.2
## [5] gghalves_0.1.4 dplyr_1.1.2 see_0.7.5 forcats_1.0.0
## [9] ggalluvial_0.12.5 ggplot2_3.4.2 SeuratObject_4.1.3 Seurat_4.3.0
## [13] knitr_1.43
##
## loaded via a namespace (and not attached):
## [1] RColorBrewer_1.1-3 rstudioapi_0.14 jsonlite_1.8.4
## [4] magrittr_2.0.3 spatstat.utils_3.0-3 farver_2.1.1
## [7] rmarkdown_2.21 vctrs_0.6.2 ROCR_1.0-11
## [10] spatstat.explore_3.2-1 webshot_0.5.4 htmltools_0.5.5
## [13] sass_0.4.6 sctransform_0.3.5 parallelly_1.35.0
## [16] KernSmooth_2.23-21 bslib_0.4.2 htmlwidgets_1.6.2
## [19] ica_1.0-3 plyr_1.8.8 plotly_4.10.1
## [22] zoo_1.8-12 cachem_1.0.8 igraph_1.4.2
## [25] mime_0.12 lifecycle_1.0.3 pkgconfig_2.0.3
## [28] Matrix_1.5-4 R6_2.5.1 fastmap_1.1.1
## [31] fitdistrplus_1.1-11 future_1.32.0 shiny_1.7.4
## [34] digest_0.6.31 colorspace_2.1-0 patchwork_1.1.2
## [37] tensor_1.5 irlba_2.3.5.1 labeling_0.4.2
## [40] progressr_0.13.0 fansi_1.0.4 spatstat.sparse_3.0-1
## [43] httr_1.4.6 polyclip_1.10-4 abind_1.4-5
## [46] compiler_4.3.0 withr_2.5.0 highr_0.10
## [49] MASS_7.3-60 tools_4.3.0 lmtest_0.9-40
## [52] httpuv_1.6.11 future.apply_1.11.0 goftest_1.2-3
## [55] glue_1.6.2 nlme_3.1-162 promises_1.2.0.1
## [58] Rtsne_0.16 cluster_2.1.4 reshape2_1.4.4
## [61] generics_0.1.3 gtable_0.3.3 spatstat.data_3.0-1
## [64] tidyr_1.3.0 data.table_1.14.8 sp_1.6-0
## [67] xml2_1.3.4 utf8_1.2.3 spatstat.geom_3.2-1
## [70] RcppAnnoy_0.0.20 ggrepel_0.9.3 RANN_2.6.1
## [73] pillar_1.9.0 later_1.3.1 splines_4.3.0
## [76] lattice_0.21-8 survival_3.5-5 deldir_1.0-6
## [79] tidyselect_1.2.0 miniUI_0.1.1.1 pbapply_1.7-0
## [82] gridExtra_2.3 svglite_2.1.1 scattermore_1.1
## [85] xfun_0.39 matrixStats_0.63.0 stringi_1.7.12
## [88] lazyeval_0.2.2 yaml_2.3.7 evaluate_0.21
## [91] codetools_0.2-19 tibble_3.2.1 cli_3.6.1
## [94] uwot_0.1.14 xtable_1.8-4 reticulate_1.28
## [97] systemfonts_1.0.4 munsell_0.5.0 jquerylib_0.1.4
## [100] Rcpp_1.0.10 globals_0.16.2 spatstat.random_3.1-5
## [103] png_0.1-8 parallel_4.3.0 ellipsis_0.3.2
## [106] listenv_0.9.0 scales_1.2.1 ggridges_0.5.4
## [109] leiden_0.4.3 purrr_1.0.1 rlang_1.1.1
## [112] cowplot_1.1.1 rvest_1.0.3 formatR_1.14